Susan. Please use the mailing list instead of personal email.
A google search for electronegativity of selenium provides a useful
first hit. The .rtp issue is covered often on the mailing list.
Overall, you will find this link helpful:
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette
Quoting Susan COSTANTINI <[email protected]>:
Dear Chris
I have read your mail regarding the selenium parameters and I have
tried to insert the SEG atom in ffG43a1.rtp but Gromacs gives error.
Where I can the electronegativities of Se?
When I run the pdb2gmx comand, Gromacs give this error:
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: pdb2gmx.c, line: 421
Fatal error:
Atom SEG in residue CYSH 50 not found in rtp entry with 8 atoms
while sorting atoms
-------------------------------------------------------
Have you idea how I can solve this problem?
Thank you in advance!!
Susan Costantini
Senior Fellow
Oncologic Center Research in Mercogliano (Italy)
I don't have the parameters. You could possibly fudge it by
extrapolating out from SER->CYS->Se_CYS based scaled by
electronegativities of O,S,Se. I'm not saying that this is rigorous,
just that its possible to do. My main point here, though, is to ask if
you *really* need to bother with this.
Thioredoxin ~ 100 amino acids. Sampling is a real problem in
simulations, and I highly doubt that you're going to see a difference
in CYS vs. Se_CYS in the context of a 100 aa protein on simulation
timescales (I also doubt you'd see a difference for CYS vs. SER).
Besides, wouldn't crystallographers be basically out of business if
Se_CYS mucked up the structure as compared to CYS?
Chris.
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